Analyst lowers third quarter iPhone estimate by 1.5 million units

But raises iPad unit sales to 3.5 million and lifts Apple price target to $349 per share

Photo: Apple Inc.

Here’s something unusual for an Apple AAPL analyst. Two weeks before the company is scheduled to announce its fiscal third quarter earnings, Kaufman Bros.’ Shaw Wu has lowered his sales estimate for Apple’s most important cash cow, the iPhone, while raising his price target for Apple’s shares.

In a note to clients issued Tuesday morning, he cut his Q3 iPhone sales estimate 16%, from 9 million units to 7.5 million.

“Based on our more detailed analysis of supply chain data,” he writes, “we are shifting our iPhone assumptions to latter quarters due to the high likelihood that an inventory drawdown and screen supply constraints could impact near-term shipments over the next two quarters. “We believe most Street estimates have not factored this in and thus we believe consensus at 8.5 million iPhones for the June quarter may likely prove too aggressive.”

Although Apple brings out a new iPhone every summer, Wu thinks this product transition is “more impactful” than previous ones because it involves two brand new phones — the iPhone 4 and the 8 GB iPhone 3GS. “With the new storage capacity, this is not as simple as taking the previous product and marking the price down.”

Meanwhile, Wu is raising several other numbers:

Q4 iPhone sales: to 10.5 million units from 10.3 million

Q3 iPad sales: to 3.5 million from 3.3 million

Apple price target: to $349 per share from $342, based on what he believes is a “reasonable” 17.5 x multiple on his estimated earnings per share for calendar 2011 of $17.35, plus net cash.

His iPod and Mac unit forecasts remain unchanged at 9.8 million and 3.2 million, respectively.